Download Review of Pedigree Programmes with Analysis

SAVE
Safeguard for Agricultural Varieties in Europe
Sicherung der landwirtschaftlichen ArtenVielfalt in Europa
Sauvegarde pour l'Agriculture des Variétés d'Europe
f o u n d a t i o n
SAVE Head Office:
Joseph-Belli-Weg 5, D-78467 Konstanz/Germany
E-mail: [email protected]
Website: http://www.save-foundation.net;
Network: http://www.agrobiodiversity.net
General Review of five PEDIGREE ANALYSIS SOFTWARE programs
One of the most important aspects in conservation programmes for endangered breeds is to
restrain the rate of inbreeding.
We will introduce you in five software programmes which may help you in a useful way to
manage your population.
The presented programmes are focusing on different target groups and have different goals of
interest.
Because of the complexity of the software we will give you some details for orientation. If you
need software help to manage your herdbook or to monitor the changes in genetic variability
and population structure you should test the software with regard to your own needs.
Animal Database ZVSN
is mainly a breeding program for the practical use in the field of conservation programmes, but
with a lot of opportunities for recording characteristics and inbreeding analyses like identifying
the genetical presence or inbreeding coefficients.
The target group are mainly Breed managers, herdbook keepers and persons responsible for
population management in conservation programs.
Kurt Steiner can be adressed directly for support, data handling and data analyses.
Breeders Assistant
is a pedigree and record keeping software program for breeders but it has also a lot tools
regarding inbreeding, mating and genetic tools like the prediction of genetic geno- and
phenotypes.
It comes with nice data integration possibilities via *.csv (Excel) and *.xml and a attractive
design, especially pedigree outputs, and reporting features. But it is a commercial program, the
personal version (modular costs) is about 130 €.
ENDOG
is a Computer Program for Monitoring Genetic Variability of Populations Using Pedigree
information.
Target group: Researchers or responsible persons for population management or teachers,
students for population genetic analysis.
Primary functions carried out by ENDOG are the computation of the individual
inbreeding (F) and the average relatedness (AR) coefficients.
Additionally, users can compute with ENDOG useful parameters in population genetics for
the number of ancestors explaining genetic variability or for the genetic importance of the herds.
Moreover, the present version of ENDOG can compute F statistics from genealogical
information.
Optimate
is a very fast Computer Program in a DOS prompt window for the registration and the simple
working on genealogic data. It is a helpful tool for breeders to give information for mating and
reducing inbreeding but the data integration is inconvenient.
PEDSYS
PEDSYS (Pedigree Database System) is a series of programs written for management and analysis
of genealogical and demographic data. It is in my opinion more a research tool and the
installation process is not very easy to understand. But it can be used on the most important
operation systems. The last version is from 1999, so it seems to be out of development now.
ChromoSoft
is a Internet Database, configurable for every association and designed as a enclosed system.
In this database, alternatively this online breeding book have all registered users access around
the clock access to the stored total population - according to your personal user rights. This
allows at any time calculations of mating and suitable proposes for mating. It also allows the
services and birth notifications. The own business can be presented, pedigrees and inbreeding
coefficients can be calculated.
Inter Herd
can be used for daily use in a dairy or meat-producing farm especially for data recording of
breeding data and health information. It is running under Windows 98 or Windows ® XP ®.
Detailed production and health data for each animal can be stored. In addition, there are daily
management plans to manage the flock effectively. Further on, a long-term analysis is possible
to observe the crop of the herd and avoid problems as well as understanding their causes. There
is also the opportunity proceeding a financial analysis of the stock inclusively other cost-control
functions.
Conclusion
The seven presented software programs are helpful tools to manage animal populations and to
avoid inbreeding. The choice for a program depends significantly of your needs and your
computer knowledge.
If you have to run a small population and you have limited budget, than Optimate may be the
right tool. If you want to do genetical analyses and you are experienced in computing and
statistics, than PEDSYS or ENDOG may be your favourites. If you have the responsibility for a
conservation program and you are not very experienced in dealing with data and analysis of
inbreeding than ZVSN with support might be your option. For a broader management of animal
population including veterinary data and an adequate reporting and contact management paired
with basic computer knowledge you might spend little money for Breeders Assistant.
Breeding clubs, or businesses with multiple locations can use the commercial software
Chromosoft if they have a limited number on individuals. Via a browser services and birth
notifications as well as proposes for mating can be calculated.
The proprietary software InterHerd works on Access basis, taking full access to the data, but not
to the formulars. This enables a further adjustment with various options for experienced users.
Multilingualism and import possibilities for data should be stressed, as well as the possibility of
further management modules to be coupled. The software is shared via Distributors (AIMS in
Germany, otherwise see http://www.interagri.org/E/distributors.htm). Prices are depending on
quotes.
Cost
Pedigree Software Programms (Technical details)
Language
Server System
Progamming
language
Name
Target group
ENDOG
Researchers or
free
responsible persons
for population
management,
teachers, students
for population
genetic analysis
englisch
Windows
95/98/2000/NT/XP
Visual Basic;
Results in MS
Access DB
75.000 75 000 records
<5min (512MB
RAM, 1.8GHzCPU)
OPTIMATE
Breed manager,
herdbook keeper
free; complete
version costs 55,Euro
german
Windows (Prompt
Mask), Windows
95/98/2000/NT/XP
Clipper, DOSSurface
99.999 50-100MB RAM are
recommended
ZVSN
Breed manager,
herdbook keeper
Windows 98
upwards/ MacOS
8.6 upwards
File Maker
30.000 32 MB RAM
upwards
PEDSYS
Research tool
Basic version about german
200,-Euro; data
integration and
support about 30,Euro
free
english
Breeders Assistant Breeders, Rare
Breed Breeders
Modular, personal
edition Breeders
Assistant (generic)
e.G. 130,- Euro
english
Windows
95/98/2000/NT/XP
Chromosoft
Breed manager,
breeder for rare
breeds, herdbook
keeper
Basis Version 366 €
+ 366€ for analysis
tools, 3 users
german
online modul via
browser
InterHerd
Farmers, herdbook
keeper
Depending on
quotes
german
Windows
98/2000/XP
Unix, Windows, Mac Fortran
OS
Data records
(tested)
Speed
30.000
1.000.000 64MB RAM upwards
html, php
Depending on
internet access
Pedigree Software Programms (General overview)
Usability
Experiences/ bugs
Download
Name
General Features
ENDOG
A Computer Program for Monitoring Genetic
Variability of Populations Using Pedigree
Information
after installation simple
Watch for correct
(pay attention to the
input data, male=1;
right allocation of correct female=2
data fields)
OPTIMATE
A Computer Program for registration and
simple working on genealogic data. A helpful
tool for breeders to give informations for
mating and reducing inbreeding.
uncomfortable DOS
orientated programm,
fast calculation of gene
rates
ZVSN
The animal database ZVSN is mainly a
breeding programm for the practical use in the
field of conservation programmes, but with
opportunites for recording characteristics and
inbreeding analyses.
PEDSYS (Pedigree Database System) is a
series of programs written for management
and analysis of genealogical and demographic
data
Breeders Assistant is a pedigree and record
keeping software program for breeders.
Programm comes out of
practical use, but a
general affinity for
computers is
indispensable
very unconvinient to
install, Status of 1999
http://www.zuchtbuchpr
ogramm.com/index.php
ftp://www.sfbr.org/pub/p
edmgt/pedsys
The program is out of
development now. Questions to:
Tierärztliche Hochschule
Hannover
Institut für Tierzucht und
Vererbungsforschung
Tel.: 0511 - 953 8582
Programming help function,
Training possible, support with
data integrating and special
programming adaptions and live
support via internet
ftp://www.sfbr.org/pub/pedmgt/pe
dsys/PSManual.pdf
can integrate and export
data e.g. via *.csv or
*.xml, very comfortable
design and data in- and
output
Chromosoft is s Internet database, alternatively Easy to undestand
a online breeding book , especially interesting
for breeding associations or clubs which want
to input their data from different sites
http://www.tenset.co.uk/
Tutorial Guide
Is a Access based software for the daily
administration of breed and health data and
additionally for financial management. It is not
a pure pedigree system
www.interagri.org
PEDSYS
Breeders
Assistant
Chromosoft
InterHerd
Training/ Support
http://www.ucm.es/info/p
rodanim/html/JP_Web_a
rchivos/Endog45.zip
easy understandable http://www.tihoand easy to install,
hannover.de/einricht/zuc
interesting for small
ht/optimate/index.htm
population, mass data
input is uncomfortable
demo version see
www.chromosoft.com
ENDOG
Pedigree Software Programms (Features)
OPTIMATE
ZVSN
PEDSYS
(F) individual
Pedigrees for 4
inbreeding Wright 1931 generations
Genetical presence
Pedigree Management
(8 programs)
(AR) Average
relatedness, GoyacheGutierrez
Calculation of
inbreeding coefficient
from 2 up to 11
generations
Inbreeding coefficient
Finds common
ancestors for selected
probands
Inbreeding per
Generation
calculation of
inbreeding for a
planned mating
Pedigree Content
Founders
Partial Inbreeding
Extensive and praxis
orientated data input
management
(Arrangement, ancestors,
offspring, inbreeding,
distribution
Coefficients of
animal-project-person
relationships between relationships, achievement
groups and
census, assesment
individuals
Detection of the most Rich search mask with the
important ancestors
possibility to refine the
search (upt to 20 steps)
Listing of all
Print with layouts for
offsprings for every
adress reports, genetical
individual
presence, inbreeding
coefficients
Generation intervals
Extensive checks of
plausibility
Offspring analysis
Lots of characteristics
can be recorded
grouping functions, interim
grouping
Identifies pedigrees and
assigns individuals to
them
Breeders Assistant
It includes fully
customizable printed
pedigrees, text, image,
HTML and circular
pedigrees.
Many features for
linechasers,
kennel/cattery
management and
comprehensive record
keeping.
calculation of Wright's
inbreeding coefficient.
Determines contribution range of Reports
of founders to
available including
subsequent generations ancestor and
descendant analyses
Transforms pedigree
contracts/agreements
data into Master File
area
format
Calculates inbreeding,
store all animal details,
kinship coefficients
contacts, show
(Quaas-Henderson)
records, litters, vet
records, vaccinations,
accounts and
appointments/tasks.
Constructs extended
genetics tools e.g.
pedigrees for specified
prediction of genotypes
probands
(coat color genetics,
carried traits +
diseases via simulation
of Mendelian genetics)
Creates Pedigree/Draw calculation of
formatted file from
inheritance probability
PEDSYS records
of specific genes
Chromosoft
InterHerd
Chromosoft is a record Flock management
keeping software,
software, no Pedigree
interesting for keepers Software!
at different locations
Data input is made by
Internet, which means
different persons can
input birth notifications
from different stations
In combination with the
Modul InterTrace is a
full traceability is
possible
Search & professional
search
The focus lays on
health and financial
management
Saving of the search
results
Daily event list with
health checks and
planned measures
Description and
advertisement site for
breeding associtations
Administration tool for
birth and services
notifications
Lactat part of the milk
is presentable as a
graphics
Graphics of fertility
Calculation of the
inbreeding coefficient
of all known ancestors,
virtual offsprings etc.
Pedigree visualisation
Pedigree Software Programms (Features)
ENDOG
Subpopulations
Coancestry
OPTIMATE
Descriptive statistics
and frequency
distribution for every
animal and individual
can be computed
Export to *.csv or *.doc
Breeding Animals
Print report
Individual Pedigree
Population Structure by
Herds
Supplying fathers,
Grandfathers
ZVSN
PEDSYS
Assembles data for EGO,
FA and MO on same
record
Breeders Assistant
modelling of polygenic
traits and various
statistical analyses
Genetic Management (7
programs)
Simplifies genotypic
structure by combining
alleles
Calculates gene and
genotype frequencies from
phenotypic data
Generates a
Phenotype/Genotype map
file
matings
Infers unknown genotypes
from genotypes of
relatives
Simplifies extended
pedigrees for genetic
analysis
Generates a peeling
sequence from an indexed
pedigree file
Tallies offspring genotypes
by parental mating type
Gene Frequency
Analysis
Covariance Analysis
between relatives
Inbreeding: The depth
at which the furthest
ancestor was found,
How many generations
of ancestors, Total
number of ancestors
found, Total number of
unique ancestors,Total
number of ancestors
common to both sides
of the pedigree
backup and restoring
opportunities